[Chimera-users] HBond on every frames of a large trajectory

Elaine Meng meng at cgl.ucsf.edu
Fri Apr 22 14:41:15 PDT 2016

Hi Jérémie,
I suspect the problems may be due to the large data size rather than using the hbonds command in per-frame scripting.  It is common to combine hbonds with per-frame scripting of trajectories... it’s even in a tutorial:


However, if you had a specific example of what you mean by not working, and the problem is reproducible (say on a smaller dataset that you could easily share with us), you could use menu: Help… Report a Bug.

I’ll have to leave it to others with no-GUI scripting experience to say whether there is a way to get these results without displaying the trajectory frames.
Sorry about the difficulties,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 22, 2016, at 9:30 AM, Jérémie KNOOPS [531802] <Jeremie.KNOOPS at umons.ac.be> wrote:

> Hi,
> What is the easiest and fastest way to get the number of H bonds on every frame of a large trajectory (>10 000 frames) and print it to a file? 
> The hbonds command does not seem to work with the perframe command and displaying the whole trajectory to run a per-frame script is quite slow.
> Jérémie Knoops
> PhD Student

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